[gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ?

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 16 11:34:15 CET 2011

On 2011-03-16 11.29, maria goranovic wrote:
> Hello
> I am trying to pdb2gmx with a free amino acid in amber99sb as follows:
> pdb2gmx -f temp.pdb -ff amber99sb
> there are no ter records in the input pdb file.
> However, pdb2gmx fails with the following error:
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.3
> Source code file: pdb2gmx.c, line: 284
> Fatal error:
> In the chosen force field there is no residue type for 'GLU' as a
> starting terminus
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Is this some kind of bug. If so, is there a workaround? For example, can
> I have the amino acid bound to the terminus of the larger protein (for
> which the free amino acid is a ligand) and make the bond have a zero
> spring constant or something?

This is a missing feature in the FF. Since charges are different for 
N-terminal and C-terminal residues in Amber there are separate 
N-terminal and C-terminal variants of (almost) all residues, but not for 
isolated AA. Your best bet is to use Antechamber to make a GAFF 
topology which you can convert to gromacs again.
> Maria
> Maria G.
> Technical University of Denmark
> Copenhagen

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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